My use for it is to backup our databases several times per day and have each backup to be saved uniquely and fully (not just files that were changed), and to not overwrite the previous download.

I've learned the scheduling features, but it just keeps overwritting the previous backup. I need it so each time the scheduler runs, it will create a new complete download like so.

Folder
Folder_1
Folder_2

This feature seems to be present for manual transfers, it prompts you so you can 'Copy and keep both files' and it appends each folder in a numerical sequence. But with scheduler I haven't been able to do this.

Of course. Edit the transfer queue item you have scheduled. You can use the following variables for the destination file/folder:
// *a Abbreviated weekday name
// *A Full weekday name
// *b Abbreviated month name
// *B Full month name
// *d Day of month as decimal number (01 – 31)
// *H Hour in 24-hour format (00 – 23)
// *I Hour in 12-hour format (01 – 12)
// *j Day of year as decimal number (001 – 366)
// *m Month as decimal number (01 – 12)
// *M Minute as decimal number (00 – 59)
// *S Second as decimal number (00 – 59)
// *U Week of year as decimal number, with Sunday as first day of week (00 – 53)
// *w Weekday as decimal number (0 – 6; Sunday is 0)
// *W Week of year as decimal number, with Monday as first day of week (00 – 53)
// *y Year without century, as decimal number (00 – 99)
// *Y Year with century, as decimal number

So for example you would set the destination to:
C:\Downloads\My Folder *d.*m.*Y

Ok, i've installed the SDK and set the script. It's now creating new items in the transfer queue, but they are not processing. No matter what I do (clicking play, pause etc)I can't get them to download. I'd like to use this with the scheduler to download a full copy of our datbase every hour. When I remove the script it downloads just fine, with the expection of the destination path is always the same. When I put the script back in no download happens, it just creates new items.